Pecorino Flashcards
Hallmarks of cancer
- Capability for autonomous growth signals 2. Evasion of growth inhibitory singals 3. Evasion of apoptotic cell death 4. Unlimited replicative potential 5. Angiogenesis 6. Invasion and metastasis
Enabling characteristics of cancer
Crucial for acquiring the six hallmarks of cancer 1. Genome instability 2. Tumor promoting inflammation
Emerging hallmarks of cancer
- Reprogramming energy metabolism 2. Avoiding immune destruction
Oncogenes - dominant or recessive
Dominant - mutation in only one allele sufficient for an effect
Tumor suppressor genes - dominant or recessive
Recessive - one intact allele generally enough to inhibit growth - Supports “two hit” hypothesis of carcinogenesis
Haploinsufficiency
Idea that rather than tumor suppressor genes being recessive, only one mutated allele may be enough to induce cancer phenotype - Normal allele produces 1/2 the normal protein product which is not enough to suppress tumor formation
Ras function
intracellular transducer protein - acts subsequently to binding of a growth factor to its receptor - Involved in transmitting the signal from the receptor through the cell
Ras is a ___ protein
G protein - activated by exchange of GDP to GTP
p53 normal role
Coordinates responses of the cell (cell cycle arrest, DNA repair, apoptosis) to different types of stress (DNA damage, hypoxia)
p53 is a ___ and acts as a ___
- Tumor suppressor gene - Acts as a transcription factor - induces expression of genes required to carry out its function
retinoblastoma gene (Rb) is a
Tumor suppressor gene
Rb function
Central role in regulating the cell cycle - Inhibits cell proliferation by binding to and suppressing an essential transcription factor of cell cycle progression
Rb activity regulated by
Phosphorylation by cyclin D and the cyclin-dependent kinases (4/6)
Small localized areas of hypermutation
Kataegis
One-off cell crisis that shatters chromosomes and result in 10-100’s of genomic rearrangements
Chromothripsis
Transitions and transversions are what type of mutation?
Base substitutions
Transitions substitute a ___ for a ___
Purine/Purine
Transversions substitute ___ for ___
Purine/Pyrimidine
What is “wobble” and “deceneracy” in the genetic code?
3rd nucleotide of a codon may be changed and new codon may code for same amino acid
Alpha particles are made of
2 protons and 2 neutrons
Beta particles are made of
electrons
X-rays are ___ radiation vs alpha particles that are ___ radiation
- low-linear energy transfer (LET) 2. high-LET
___-LET radiation more commonly causes DSBs and lead to chromosomal translocations and deletions
High
Ionizing radiation therapy includes
- alpha and beta particles - gamma rays
How does ionizing radiation cause DNA damage?
- Indirect - interacts with atoms, ejects e-, causes an ion to form, interacts with water (radiolysis) –> ROS 2. DNA directly ionized
What are the 3 ROS formed by ionizing radiation therapy
Hyroxyl (OH) Hydrogen peroxide (H2O2) Superoxide (O2-)
Which type of UV radiation is the most effective carcinogen?
UVB`
___ are responsible for the majority of UVB induced mutations
Cyclobutane pyrimidine dimers
UVA ___damages DNA via___
- Indirectly - Free-radical mediated damage
___ transversions are characteristic of UVA damage
G-T
Common MOA of chemical carcinogens
Electrophilic (electron-deficient) form reacts with nucleophilic sites (donate electrons) in purine and pyrimidine rings of nucleic acids
Example of polycyclic aromatic hydrocarbons (PAH)
Benzo(a)pyrene - major well-known carcinogen in cigarettes
Heterocyclic amines are
carcinogens produced by cooking meat
One-step DNA repair
- Direct reversal of DNA damage - Removal of alkyl group from the O6 atom of guanine after exposure of DNA to alkylating carcinogens
What DNA repair enzyme is involved in one-step DNA repair?
Alkyltransferase
What type of DNA damage does NER repair
Helix-distorting lesions - bulky DNA adducts induced by environmental agents (UVV, PAHs)
Two subpathways of NER
- Global genome NER (for helix distortion) 2. Transcription-coupled repair (damage interfering with transcription)
Describe the process of repair by NER
- Lesion + adjacent nucleotide excised by endonucleases 2. DNA polymerase delta/epsilon fills gap with opposite strand as template (proliferating cell nuclear factor is part of polymerase holoenzyme and physically forms ring that encircles and binds the damaged region
What DNA polymerase is used in NER
delta(δ )/epsilon(ε)
What does NER stand for?
Nucleotide excision repair
What genetic disease is characterized by a defect in NER?
Xeroderma pigmentosum (XP)
What does BER stand for?
Base excision repair
What does BER repair?
Targets chemically altered bases induced primarily by endogenous mechanisms - w/o BER, would cause a point mutation
Describe the steps of BER
- DNA damage-specific glycosylases (OGG1 and MUTYH) scan bases for 8-oxoguanine lesions - Lesion is flipped out of the helix and cleaved –> abasic site - Endonuclease cleaves DNA strand at abasic site - DNA polymerase β replaces nucleotide, ligase fills gap
What does PARP stand for?
poly(ADP-ribose) polymerase
What role does PARP play in BER
Interacts with single strand break intermediates formed during BER –> poly(ADP-ribose) chains –> signals to other DNA repair proteins and leads to modification of histones –> relaxed chromatin structure for increased DNA accessibility
What type of DNA damage does mismatch repair fix
Replication errors that have escaped editing by polymerases - includes repair of insertions and deletions produced as a result of slippage during repair of repetitive sequences and nucleotide mismatches
Describe the steps in mismatch repair
- mismatch recognized by hMSH2/6 and hMSH2/3 2. hMLH1/hPMS2 and hMHL1/hPMS1 recruited 3. Endonucleases and exonucleases removed nucleotides around and including the mismatch DNA polymerases resynthesizes a newly replicated strand
What human cancer syndrome commonly has loss of mismatch repair
Hereditary non-polyposis colorectal cancer
What are the two types of recombinational DNA repair
Homologous repair and non-homologous end-joining
What type of DNA damage does recombinational repair fix
double-strand DNA breaks
What does homologous recombination require
The presence of sister chromatids formed during DNA synthesis - template for recombining severed ends
What kinase is activated by DSBs in HR?
ataxia telangiectasia mutated (ATM) kinase
What substrate does ATM act on
RAD50/MRE11/NBS1 complex –> 5’-3’ exonuclease activity creates 3’ DNA ends
What aids in nuclear transport of RAD51
BRCA1/2
What does RAD51 do in HR
Binds to exposed 3’ ends (facilitated by RAD52) –> exchanges a homologous sequence from a single strand w/in a double stranded molecule (i.e. sister chromatid)
Junctions formed as a result of HR
Holliday junctions
Which form of recombinational repair is error prone and which is very unlikely to form errors?
- Error prone = non-homologous end-joining 2. Rare errors = homologous recombination
What inherited disease causes defective HR and makes patients sensitive to x-rays?
Ataxia telangiectasia - mutation in ATM kinase
Clinically used antimetabolites
Methotrexate, 5-fluorourail (5-FU)
5-FU MOA
Antimetabolite Derivative of uracil -> converted to fluorodeoxyuridylate (F-dUMP) - competes with natural substrate dUMP for catalytic site of thymidylate synthase (inactivates) –> depletes dTMP and dTTP –> dUMP and dUTP accumulate –> DNA synthesis in rapidly dividing cells compromised
F-dUMP competes with ___ for catalytic site of _____
dUMP thymidylate synthase
Thymidylate synthase produces
deoxythymidylate (dTMP)
Methotrexate MOA
Antimetabolite Competitive inhibitor of dihydrofolate reductase
What does dihydrofolate reductase do?
Regenerates tetrahydrofolate which produces N5N10 methylenetetrahydrofolate that is required in thymidylate synthase reaction
Vincristine and Vinblastine bind to ____ and do what?
Tubulin Prevent microtubule assembly
Paclitaxel binds to ___ and does what?
Beta-tubulin subunit in polymers Stabilizes microtubules against depolymerization
What can assist in making radiation-induced damage permanent?
Oxygen Also, more DS breaks occur in cells irradiated in presence of oxygen than in those without
Mechanisms of chemotherapy resistance
Increasing drug efflux Decreasing intake of drug Increasing the number of target molecules within the cell Altering drug metabolism or DNA repair processes
MDR codes for ____?
P-glycoprotein (P-gp)
P-glycoprotein is____ and its MOA is ____
Chloride ion efflux pump ATP hydrolyzed –> conformational change of P-gp–> drug released extracellularly
PARP inhibitors are used in tumors with ____ mutations
BRCA1/2
Inhibition of PARP causes impaired…
base excision repair and the accumulation of SS DNA breaks that can lead to DS breaks (normally repaired by homologous recombination pathways
BRCA1 or BRCA2 mutations cause deficiency in…
homologous recombination and DS repair
Four common types of DNA-binding domains
helix-turn-helix motif Leucine zipper helix-loop-helix motif zinc finger motif
T/F: misregulation of a single transcription factor can cause cancer
T
AP-1 transcription factor is important in
Processes of growth, differentiation and death –> therefore plays a role in carcinogenesis
AP-1 binds:
12-O-tetradecanoylphorbol-13-acetate (TPA) response element or cAMP response element
AP-1 transcription factor is composed of ___ components and can be produced by dimers of proteins from the ___ and ____ families
two; Jun and Fos
Jun acts as __1__ of proliferation, Jun B acts as a __2__ in the presence of __3__
- Positive regulator of proliferation 2. Negative regulator 3. Jun
Where in the cell do steroid hormones work?
Pass through cell membrane, bind intracellular receptors in cytoplasm
What makes up the histone core?
Two copies of histones H2A, H2B H3 and H4
What are the two main types of epigenetic mechanisms
- Histone modifications
- DNA methylation
What are the main post-translational modifications that can happen to histones?
Acetylation
Methylation
Phosphorylation
Ubiquination
What are the two families of enzymes that participated in acetylation of histones?
Histone acetyltransferases (HATs - add acetyl)
Histone deacetylases (HDACs - remove acetyl)
What does histone acetylation do?
Neutralizes positive charge on lysine residues –> relaxes chronmatin –> more transcription
What does histone deacetylation do?
Restores positive charge to lysine in histone tails –> compacted chromatin –> less transcription
What tumor suppressor gene works in part through acetyl modification of histones? Which enzyme does it recruit to do this?
RB
HDACs
Where does DNA methylation occur?
Position 5 of cytosine only at cytosine nucleotides that are situated 5’ to guanine nucleotides (CpGs)
Where are CpG isloands commonly located? What is their methylation status?
Promoter region of genes
Usually non methylated –> transcription can occur
What enzymes mediate DNA methylation?
DNA methyltransferases (DNMTs)
Are DNA methylation patterns inheritable?
Yesh.
Areas of chromatin that are relaxed are indicative of ___ and are associated with ____ mutation density.
active transcription
low
DNA hypo/hyper methylation has been observed in normally unmethylated/methylated CpG islands of gene promoters in cancer
hypermethylated
unmethylated
Gene silencing by ____ may be an important mechanism of carcinogenesis by which critical genes such as ____ are turned off
Methylation
Tumor Suppressor
Key genes affected by DNA methylation in cancer
Rb
p16INK4a (inhibits cell cycle)
pro-apoptotic death-associated protein kinase (DAPK)
What is a non-genotoxic carcinogen?
Agents that do not mutate genes but are rather epigenetic carcinogens
ex: phenobarbital in mice
Is the genome of a cancer cell generally hypo or hypermethylated?
Overall HYPOmethylated
Hypermethylation in specific gene promoters
What are microRNAs (miRNA) and what do they do?
small, non-protein coding RNAs
Regulate the expression of mRNA - powerful regulators of gene expression (repress genes)
What are telomeres composed of?
TTAGGG sequences bound by shelterin complex
What does telomerase do?
Maintains telomere length in certain cell types
Reverse transcriptase that has complementary base pairs to the TTAGG repeats in telomeres
Maintenance of ___ important for cancer cell immortality and tumor growth which is commonly accomplished by upregulating ____
Telomeres
Telomerase
What drugs are used to target DNA methyltransferases and what do they do?
5-azacytidine (5-azaC), 5-aza-2’-deoxycytidine
Bind DNA methyltransferases –> significant demethylation
What are the four types of proteins involved in transduction of a growth factor signal
growth factors
growth factor receptors
intracellular signal transducers
nuclear transcription factors
Many growth factors are
tyrosine kinases
What are EGF receptors also called?
ErbB or HER (1-4)
What is unique about HER2 compared to other EGFRs
HER2 doesn’t bind to a ligand but is a co-receptors for other EGFRs; other EGFRs are receptor tyrosine kinases
What are the six steps of EGF signalling
- Binding of growth factor to receptor
- Receptor dimerization
- Autophosphorylation
- Activation of intracellular transducers - includes RAS
- Activation of a cascade of serine/threonine kinases (Raf, MEK, MAPK)
- Regulation of transcription factors for gene expression
What does dimerization of EGFRs cause
Changes shape of receptor allowing access of ATP and substrate to the catalytic kinase domain –> autophosphorylation from on dimer to the other
What activates RAS
Son of Sevenless (SOS)
Src homology (SH2 and SH3) domains on Grb2 recognize phosphyorylated EGFR –> interact with son of sevenless (SOS) –> activates RAS
What kind of molecule is RAS
GTP-binding protein
GTP-binding proteins are inactive when they are bound to ____ and active when bound to ____
GDP
GTP
What does son of sevenless (SOS) do?
Activates RAS by mediating exchage of GDP to GTP
What is farnesylation
Addition of C15 farnesyl isoprenoid lipid to RAS and is required for localizing RAS to the cell membrane
What does activated RAS (RAS-GTP) bind to
Raf
What kind of molecule is Raf?
Serine/threonine kinase
Raf is one of the main effectors of
RAS
Raf phosphorylates what?
mitogen-activated protein kinase kinase (MAPKK or MEK)
What kind of molecule is MAPKK
Dual tyrosine and serine/threonine kinase
What does activated MAPPKK (MEK) do?
Phosphorylates mitogen-activated protein kinases (MAPKs, aka ERKs)
What do MAPKs do
Provide cytoplasmic link between activated RAS on plasma membrane and regulation of gene expression because MAPKs can enter the nucleus
What is AP-1
Transcription factor - binds DNA and regulates expression of genes involved in growth, differentiation and death
Target of MAPK cascade
What does AP-1 bind to
cyclin D gene - critical regulator of the cell cycle
What gene families make up AP-1
jun and fos
What are the Myc family of molecules
Transcription factors - Myc, Max, Mad, Mxi
Targets of MAPK
What are some of the gene targets of Myc?
N-Ras, p53
What is phosphatidylinositol 3-kinase (PI3K)
Lipid kinase, effector protein downstream of RAS
Interaction of RAS with PI3K results in production of
a second messenger, PIP3
What does PIP3 recruite and what kind of molecule is it?
PDK-1
serine/threonine kinase
What does PDK-1 do
phosphorylates Akt
What is Akt and what does it do?
serine/threonine kinase
anti-apoptotic and survival roles by phosphorylating distinct target proteins; ex: m-TOR
What is SRC?
Intracellular tyrosine kinase
Roles in cell proliferation, regulation of cell adhesion, invasion and motility
What can activate SRC? What does activated SRC do?
EGF receptor; focal adhesion kinase (FAK)
Activation of SRC leads to disassembly of focal adhesions –> increased cell motility
Inhibits E-cadherin (important for cell invasion)
Oncogenes are dominant or recessive?
Dominant
PDGF can act as a oncogene or tumor suppressor gene?
Oncogene - aberrant location in cytoplasm instead of secreted
what does the oncogene v-erbB do?
Makes mutated EGFR that triggers cell division w/o EGF binding
RAS as an oncogene
Loss of GTPase activity of RAS protein –> constiutive activation of RAS
Most commonly mutated form of B-Raf? What does it do?
V600E
Causes constitutive kinase activity and insensitivity to feedback mechanisms –> abnormal cell growth
How does BCR-ABL work as an oncogene
Fusion protein BCR-ABL maintained in cytoplasm –> nuclear kinase constitutively activated where it shouldn’t be and interferes with normal signal transduction pathways
How does Imatinib (Gleevec) work?
Binds ATP-binding pcoket w/in catalytic domain –> preferential binding to inactive state of kinases
Works against PDGFR, ABL and c-Kit
Four stages of the cell cycle
- G1
- S phase
- G2
- M phase
What stages make up interphase
G1, S, G2
What is G0
G0 = quiescent state, outside cell cycle
Passage through the different phases of the cell cycle is regulated by
Cyclins and cyclin-dependent kinases
When cyclins bind to cdks, they ___ the cdk
activate
Which cyclins drive progression through G1
Cyclin D + cdk 4/6
What does cyclin D do?
regulates expression of cyclin E gene (product is important for G1 to S transition)
at cyclin-cdk is important for S phase progression
Cyclin A-cdk2
What cyclin-cdk directs G2 and the G2 to M phase transition
Cyclins A, B-cdk1
G1 check point leads to cell cycle arresnt in response to what?
DNA damage - ensures DNA isn’t replicated in S phase
The G2 checkpoint leads to arrest of the cell cycle in response to what
Damaged and/or unreplicated DNA - ensures proper completion of S phase
M checkpoint leads to arrest of chromosomal segregation in response to what
misalignment of the mitotic spindle
How to cyclins/cdks exert their effects
Phosphorylating target proteins
What two processes predominantly control cell cycle progression?
- protein phosphorylation and dephosphorylation by kinases and phosphatases
- Specific proteolytic degradation targeted by the addtion of ubiquitin to the proteasome